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PDB files can describe molecular structures in atomic detail

The Brookhaven Protein Data Bank (PDB) format is a common system for specifying molecular structures, here listing first all the atoms (with types and coordinates), then all the bonds. Below is the content of a PDB file for the small sleeve bearing shown to the left. Note that this is a fixed-column, punchcard-oriented format — PDB is an old standard; there are many others.

 
COMPND  SmallBearing.pdb                                                     
HETATM    1  C                  -2.937  -5.893   1.219                
HETATM    2  C                  -2.553  -5.098  -0.109                
HETATM    3  C                  -2.947  -5.889  -1.437                
HETATM    4 Si                  -4.839  -5.890   1.063                
HETATM    5 Si                  -4.846  -5.890  -1.270                
HETATM    6  O                  -3.107  -3.761  -0.102                
HETATM    7  C                  -5.203  -4.021   1.234                
HETATM    8  C                  -4.524  -3.488  -0.104                
HETATM    9  C                  -5.204  -4.022  -1.441                
HETATM   10 Si                  -6.928  -3.219   1.063                
HETATM   11 Si                  -6.930  -3.223  -1.270                
HETATM   12  O                  -4.445  -2.045  -0.105                
HETATM   13  C                  -6.464  -1.375   1.224                
HETATM   14  C                  -5.610  -1.189  -0.109                
HETATM   15  C                  -6.464  -1.382  -1.440                
HETATM   16 Si                  -7.658   0.106   1.054                
HETATM   17 Si                  -7.661   0.096  -1.280                
HETATM   18  O                  -4.918   0.080  -0.109                
HETATM   19  C                  -6.439   1.568   1.212                
HETATM   20  C                  -5.591   1.359  -0.120                
HETATM   21  C                  -6.441   1.553  -1.454                
HETATM   22 Si                  -6.877   3.417   1.035                
HETATM   23 Si                  -6.881   3.403  -1.300                
HETATM   24  O                  -4.414   2.200  -0.127                
HETATM   25  C                  -5.140   4.196   1.197                
HETATM   26  C                  -4.470   3.643  -0.137                
HETATM   27  C                  -5.145   4.178  -1.477                
HETATM   28 Si                  -4.745   6.057   1.014                
HETATM   29 Si                  -4.752   6.042  -1.320                
HETATM   30  O                  -3.049   3.895  -0.141                
HETATM   31  C                  -2.843   6.031   1.169                
HETATM   32  C                  -2.472   5.222  -0.155                
HETATM   33  C                  -2.852   6.013  -1.487                
HETATM   34 Si                  -1.659   7.516   0.993                
HETATM   35 Si                  -1.669   7.500  -1.339                
HETATM   36  O                  -1.081   4.822  -0.158                
HETATM   37  C                   0.029   6.633   1.163                
HETATM   38  C                   0.015   5.763  -0.170                
HETATM   39  C                   0.015   6.616  -1.513                
HETATM   40 Si                   1.729   7.487   0.977                
HETATM   41 Si                   1.716   7.474  -1.355                
HETATM   42  O                   1.095   4.804  -0.169                
HETATM   43  C                   2.891   5.983   1.140                
HETATM   44  C                   2.492   5.181  -0.180                
HETATM   45  C                   2.874   5.967  -1.515                
HETATM   46 Si                   4.791   5.976   0.967                
HETATM   47 Si                   4.776   5.964  -1.366                
HETATM   48  O                   3.047   3.843  -0.174                
HETATM   49  C                   5.154   4.107   1.145                
HETATM   50  C                   4.464   3.568  -0.184                
HETATM   51  C                   5.133   4.094  -1.530                
HETATM   52 Si                   6.878   3.303   0.964                
HETATM   53 Si                   6.859   3.292  -1.369                
HETATM   54  O                   4.384   2.125  -0.175                
HETATM   55  C                   6.415   1.460   1.142                
HETATM   56  C                   5.548   1.267  -0.182                
HETATM   57  C                   6.390   1.450  -1.523                
HETATM   58 Si                   7.607  -0.022   0.970                
HETATM   59 Si                   7.585  -0.030  -1.364                
HETATM   60  O                   4.854  -0.002  -0.166                
HETATM   61  C                   6.388  -1.482   1.152                
HETATM   62  C                   5.526  -1.281  -0.173                
HETATM   63  C                   6.360  -1.486  -1.515                
HETATM   64 Si                   6.825  -3.332   0.982                
HETATM   65 Si                   6.800  -3.335  -1.351                
HETATM   66  O                   4.348  -2.118  -0.158                
HETATM   67  C                   5.090  -4.109   1.171                
HETATM   68  C                   4.404  -3.563  -0.158                
HETATM   69  C                   5.061  -4.107  -1.503                
HETATM   70 Si                   4.692  -5.971   1.004                
HETATM   71 Si                   4.670  -5.969  -1.330                
HETATM   72  O                   2.983  -3.812  -0.139                
HETATM   73  C                   2.792  -5.940   1.184                
HETATM   74  C                   2.406  -5.139  -0.140                
HETATM   75  C                   2.770  -5.935  -1.474                
HETATM   76 Si                   1.608  -7.428   1.026                
HETATM   77 Si                   1.591  -7.423  -1.306                
HETATM   78  O                   1.017  -4.737  -0.126                
HETATM   79  C                  -0.077  -6.545   1.213                
HETATM   80  C                  -0.078  -5.678  -0.123                
HETATM   81  C                  -0.094  -6.536  -1.464                
HETATM   82 Si                  -1.779  -7.400   1.048                
HETATM   83 Si                  -1.790  -7.396  -1.284                
HETATM   84  O                  -1.157  -4.719  -0.111                
HETATM  191  H                  -2.676  -5.387   2.169                
HETATM  192  H                  -2.695  -5.384  -2.390                
HETATM  193  H                  -5.617  -6.842   1.879                
HETATM  195  H                  -5.627  -6.840  -2.087                
HETATM  197  H                  -4.714  -3.634   2.154                
HETATM  199  H                  -4.717  -3.635  -2.362                
HETATM  198  H                  -8.038  -3.745   1.881                
HETATM  200  H                  -8.038  -3.752  -2.089                
HETATM  201  H                  -5.880  -1.256   2.160                
HETATM  203  H                  -5.884  -1.270  -2.378                
HETATM  202  H                  -8.889   0.119   1.869                
HETATM  204  H                  -8.891   0.100  -2.096                
HETATM  205  H                  -5.853   1.446   2.146                
HETATM  207  H                  -5.857   1.423  -2.389                
HETATM  206  H                  -7.979   3.966   1.850                
HETATM  208  H                  -7.984   3.939  -2.119                
HETATM  209  H                  -4.659   3.808   2.121                
HETATM  211  H                  -4.668   3.779  -2.397                
HETATM  210  H                  -5.508   7.027   1.824                
HETATM  212  H                  -5.521   7.000  -2.141                
HETATM  213  H                  -2.589   5.526   2.122                
HETATM  215  H                  -2.605   5.498  -2.436                
HETATM  214  H                  -1.912   8.723   1.804                
HETATM  216  H                  -1.930   8.698  -2.164                
HETATM  217  H                   0.028   6.010   2.083                
HETATM  219  H                   0.005   5.982  -2.426                
HETATM  218  H                   2.011   8.689   1.785                
HETATM  220  H                   1.989   8.666  -2.182                
HETATM  221  H                   2.641   5.485   2.097                
HETATM  223  H                   2.613   5.459  -2.463                
HETATM  222  H                   5.579   6.930   1.772                
HETATM  224  H                   5.552   6.908  -2.193                
HETATM  225  H                   4.673   3.725   2.071                
HETATM  227  H                   4.638   3.702  -2.444                
HETATM  226  H                   7.996   3.833   1.770                
HETATM  228  H                   7.963   3.813  -2.200                
HETATM  229  H                   5.843   1.348   2.085                
HETATM  231  H                   5.800   1.332  -2.455                
HETATM  230  H                   8.846  -0.032   1.772                
HETATM  232  H                   8.807  -0.045  -2.193                
HETATM  233  H                   5.811  -1.353   2.091                
HETATM  235  H                   5.765  -1.360  -2.443                
HETATM  234  H                   7.936  -3.876   1.787                
HETATM  236  H                   7.891  -3.880  -2.183                
HETATM  237  H                   4.621  -3.716   2.100                
HETATM  239  H                   4.572  -3.713  -2.420                
HETATM  238  H                   5.464  -6.937   1.810                
HETATM  240  H                   5.425  -6.931  -2.156                
HETATM  241  H                   2.548  -5.427   2.135                
HETATM  243  H                   2.511  -5.423  -2.421                
HETATM  242  H                   1.872  -8.633   1.837                
HETATM  244  H                   1.841  -8.621  -2.131                
HETATM  245  H                  -0.065  -5.920   2.132                
HETATM  246  H                  -0.094  -5.904  -2.379                
HETATM  194  H                  -2.052  -8.600   1.863                
HETATM  196  H                  -2.070  -8.590  -2.106                
HETATM  113  C                  -2.127   1.223  -2.564                
HETATM  114  C                  -2.113  -1.171  -2.551                
HETATM  115  C                  -0.060   2.432  -2.582                
HETATM  116  C                   2.020   1.247  -2.588                
HETATM  117  C                   2.034  -1.147  -2.575                
HETATM  118  C                  -0.033  -2.356  -2.555                
HETATM  119  C                  -1.359  -0.732  -3.825                
HETATM  120  C                  -1.367   0.780  -3.834                
HETATM  121  C                  -0.063   1.543  -3.845                
HETATM  122  C                   1.251   0.795  -3.849                
HETATM  123  C                   1.259  -0.717  -3.841                
HETATM  124  C                  -0.046  -1.481  -3.828                
HETATM  125  S                  -3.500   0.018  -2.756                
HETATM  126  S                  -1.790   3.016  -2.777                
HETATM  127  S                   1.661   3.036  -2.796                
HETATM  128  S                   3.404   0.057  -2.796                
HETATM  129  S                   1.695  -2.942  -2.764                
HETATM  130  S                  -1.756  -2.961  -2.743                
HETATM  131  C                  -2.100   1.249   2.317                
HETATM  132  C                  -0.032   2.458   2.298                
HETATM  133  C                  -2.085  -1.145   2.330                
HETATM  134  C                  -0.004  -2.331   2.323                
HETATM  135  C                   2.063  -1.123   2.305                
HETATM  136  C                   2.050   1.272   2.293                
HETATM  137  C                  -0.019   1.583   3.570                
HETATM  138  C                  -1.324   0.820   3.583                
HETATM  139  C                  -1.315  -0.693   3.591                
HETATM  140  C                  -0.002  -1.442   3.586                
HETATM  141  C                   1.303  -0.678   3.575                
HETATM  142  C                   1.295   0.834   3.567                
HETATM  143  S                  -1.760   3.046   2.502                
HETATM  144  S                  -3.471   0.045   2.532                
HETATM  145  S                  -1.727  -2.937   2.529                
HETATM  146  S                   1.727  -2.918   2.509                
HETATM  147  S                   3.437   0.083   2.491                
HETATM  148  S                   1.693   3.064   2.481                
HETATM  149  C                   1.286   0.824   1.024                
HETATM  150  C                  -0.034   1.575   1.028                
HETATM  151  C                  -1.346   0.809   1.040                
HETATM  152  C                  -1.337  -0.710   1.048                
HETATM  153  C                  -0.017  -1.461   1.044                
HETATM  154  C                   1.295  -0.695   1.032                
HETATM  155  O                  -0.046   2.400  -0.142                
HETATM  156  O                   1.996   1.236  -0.147                
HETATM  157  O                   2.010  -1.112  -0.134                
HETATM  158  O                  -2.074   1.214  -0.123                
HETATM  159  O                  -2.061  -1.134  -0.110                
HETATM  160  O                  -0.019  -2.298  -0.116                
HETATM  161  C                  -0.030  -1.474  -1.285                
HETATM  162  C                  -1.351  -0.722  -1.282                
HETATM  163  C                  -1.360   0.797  -1.290                
HETATM  164  C                  -0.048   1.563  -1.302                
HETATM  165  C                   1.272   0.811  -1.306                
HETATM  166  C                   1.281  -0.708  -1.297                
HETATM  167  H                  -1.931  -1.070  -4.734                
HETATM  168  H                  -1.943   1.100  -4.746                
HETATM  169  H                  -0.072   2.196  -4.762                
HETATM  170  H                   1.812   1.121  -4.768                
HETATM  171  H                   1.824  -1.048  -4.756                
HETATM  172  H                  -0.047  -2.144  -4.737                
HETATM  173  H                  -0.017   2.247   4.479                
HETATM  174  H                  -1.890   1.151   4.498                
HETATM  175  H                  -1.878  -1.020   4.509                
HETATM  176  H                   0.007  -2.096   4.502                
HETATM  177  H                   1.880  -1.000   4.487                
HETATM  178  H                   1.868   1.172   4.475                
CONECT    1    2    4   82  191                              
CONECT    2    1    3    6   84                              
CONECT    3    2    5   83  192                              
CONECT    4    1    5    7  193                              
CONECT    5    3    4    9  195                              
CONECT    6    2    8                                        
CONECT    7    4    8   10  197                              
CONECT    8    6    7    9   12                              
CONECT    9    5    8   11  199                              
CONECT   10    7   11   13  198                              
CONECT   11    9   10   15  200                              
CONECT   12    8   14                                        
CONECT   13   10   14   16  201                              
CONECT   14   12   13   15   18                              
CONECT   15   11   14   17  203                              
CONECT   16   13   17   19  202                              
CONECT   17   15   16   21  204                              
CONECT   18   14   20                                        
CONECT   19   16   20   22  205                              
CONECT   20   18   19   21   24                              
CONECT   21   17   20   23  207                              
CONECT   22   19   23   25  206                              
CONECT   23   21   22   27  208                              
CONECT   24   20   26                                        
CONECT   25   22   26   28  209                              
CONECT   26   24   25   27   30                              
CONECT   27   23   26   29  211                              
CONECT   28   25   29   31  210                              
CONECT   29   27   28   33  212                              
CONECT   30   26   32                                        
CONECT   31   28   32   34  213                              
CONECT   32   30   31   33   36                              
CONECT   33   29   32   35  215                              
CONECT   34   31   35   37  214                              
CONECT   35   33   34   39  216                              
CONECT   36   32   38                                        
CONECT   37   34   38   40  217                              
CONECT   38   36   37   39   42                              
CONECT   39   35   38   41  219                              
CONECT   40   37   41   43  218                              
CONECT   41   39   40   45  220                              
CONECT   42   38   44                                        
CONECT   43   40   44   46  221                              
CONECT   44   42   43   45   48                              
CONECT   45   41   44   47  223                              
CONECT   46   43   47   49  222                              
CONECT   47   45   46   51  224                              
CONECT   48   44   50                                        
CONECT   49   46   50   52  225                              
CONECT   50   48   49   51   54                              
CONECT   51   47   50   53  227                              
CONECT   52   49   53   55  226                              
CONECT   53   51   52   57  228                              
CONECT   54   50   56                                        
CONECT   55   52   56   58  229                              
CONECT   56   54   55   57   60                              
CONECT   57   53   56   59  231                              
CONECT   58   55   59   61  230                              
CONECT   59   57   58   63  232                              
CONECT   60   56   62                                        
CONECT   61   58   62   64  233                              
CONECT   62   60   61   63   66                              
CONECT   63   59   62   65  235                              
CONECT   64   61   65   67  234                              
CONECT   65   63   64   69  236                              
CONECT   66   62   68                                        
CONECT   67   64   68   70  237                              
CONECT   68   66   67   69   72                              
CONECT   69   65   68   71  239                              
CONECT   70   67   71   73  238                              
CONECT   71   69   70   75  240                              
CONECT   72   68   74                                        
CONECT   73   70   74   76  241                              
CONECT   74   72   73   75   78                              
CONECT   75   71   74   77  243                              
CONECT   76   73   77   79  242                              
CONECT   77   75   76   81  244                              
CONECT   78   74   80                                        
CONECT   79   76   80   82  245                              
CONECT   80   78   79   81   84                              
CONECT   81   77   80   83  246                              
CONECT   82    1   79   83  194                              
CONECT   83    3   81   82  196                              
CONECT   84    2   80                                        
CONECT  191    1                                             
CONECT  192    3                                             
CONECT  193    4                                             
CONECT  195    5                                             
CONECT  197    7                                             
CONECT  199    9                                             
CONECT  198   10                                             
CONECT  200   11                                             
CONECT  201   13                                             
CONECT  203   15                                             
CONECT  202   16                                             
CONECT  204   17                                             
CONECT  205   19                                             
CONECT  207   21                                             
CONECT  206   22                                             
CONECT  208   23                                             
CONECT  209   25                                             
CONECT  211   27                                             
CONECT  210   28                                             
CONECT  212   29                                             
CONECT  213   31                                             
CONECT  215   33                                             
CONECT  214   34                                             
CONECT  216   35                                             
CONECT  217   37                                             
CONECT  219   39                                             
CONECT  218   40                                             
CONECT  220   41                                             
CONECT  221   43                                             
CONECT  223   45                                             
CONECT  222   46                                             
CONECT  224   47                                             
CONECT  225   49                                             
CONECT  227   51                                             
CONECT  226   52                                             
CONECT  228   53                                             
CONECT  229   55                                             
CONECT  231   57                                             
CONECT  230   58                                             
CONECT  232   59                                             
CONECT  233   61                                             
CONECT  235   63                                             
CONECT  234   64                                             
CONECT  236   65                                             
CONECT  237   67                                             
CONECT  239   69                                             
CONECT  238   70                                             
CONECT  240   71                                             
CONECT  241   73                                             
CONECT  243   75                                             
CONECT  242   76                                             
CONECT  244   77                                             
CONECT  245   79                                             
CONECT  246   81                                             
CONECT  194   82                                             
CONECT  196   83                                             
CONECT  113  120  125  126  163                              
CONECT  114  119  125  130  162                              
CONECT  115  121  126  127  164                              
CONECT  116  122  127  128  165                              
CONECT  117  123  128  129  166                              
CONECT  118  124  129  130  161                              
CONECT  119  114  120  124  167                              
CONECT  120  113  119  121  168                              
CONECT  121  115  120  122  169                              
CONECT  122  116  121  123  170                              
CONECT  123  117  122  124  171                              
CONECT  124  118  119  123  172                              
CONECT  125  113  114                                        
CONECT  126  113  115                                        
CONECT  127  115  116                                        
CONECT  128  116  117                                        
CONECT  129  117  118                                        
CONECT  130  114  118                                        
CONECT  131  138  143  144  151                              
CONECT  132  137  143  148  150                              
CONECT  133  139  144  145  152                              
CONECT  134  140  145  146  153                              
CONECT  135  141  146  147  154                              
CONECT  136  142  147  148  149                              
CONECT  137  132  138  142  173                              
CONECT  138  131  137  139  174                              
CONECT  139  133  138  140  175                              
CONECT  140  134  139  141  176                              
CONECT  141  135  140  142  177                              
CONECT  142  136  137  141  178                              
CONECT  143  131  132                                        
CONECT  144  131  133                                        
CONECT  145  133  134                                        
CONECT  146  134  135                                        
CONECT  147  135  136                                        
CONECT  148  132  136                                        
CONECT  149  136  150  154  156                              
CONECT  150  132  149  151  155                              
CONECT  151  131  150  152  158                              
CONECT  152  133  151  153  159                              
CONECT  153  134  152  154  160                              
CONECT  154  135  149  153  157                              
CONECT  155  150  164                                        
CONECT  156  149  165                                        
CONECT  157  154  166                                        
CONECT  158  151  163                                        
CONECT  159  152  162                                        
CONECT  160  153  161                                        
CONECT  161  118  160  162  166                              
CONECT  162  114  159  161  163                              
CONECT  163  113  158  162  164                              
CONECT  164  115  155  163  165                              
CONECT  165  116  156  164  166                              
CONECT  166  117  157  161  165                              
CONECT  167  119                                             
CONECT  168  120                                             
CONECT  169  121                                             
CONECT  170  122                                             
CONECT  171  123                                             
CONECT  172  124                                             
CONECT  173  137                                             
CONECT  174  138                                             
CONECT  175  139                                             
CONECT  176  140                                             
CONECT  177  141                                             
CONECT  178  142                                             
END